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/**
* BioJava development code This code may be freely distributed and modified
* under the terms of the GNU Lesser General Public Licence. This should be
* distributed with the code. If you do not have a copy, see:
* http://www.gnu.org/copyleft/lesser.html Copyright for this code is held
* jointly by the individual authors. These should be listed in
*
*@author doc comments. For more information on the BioJava project and its
* aims, or to join the biojava-l mailing list, visit the home page at:
* http://www.biojava.org/
*/
package org.biojava.bio.program.sax.blastxml;
import org.biojava.bio.seq.io.game.ElementRecognizer;
import org.biojava.utils.stax.StAXContentHandler;
import org.biojava.utils.stax.StringElementHandlerBase;
import org.xml.sax.Attributes;
import org.xml.sax.SAXException;
import org.xml.sax.helpers.AttributesImpl;
/**
* This class handles the element in NCBI Blast XML.
* It generates events of the type handled by SearchContentHandler.
* Most events will be generated just using the element local name
* as the key and the CDATA as the value.
*
* The events do not conform to the BlastLikeDataSetCollection DTD
* conformity is achieved with an adaptor class that intercepts
* certain event types and translates them to that used in the
* above DTD. This was done to focus all the changes necessary
* to achieve conformity in the adaptor class.
*/
class HspHandler
extends StAXFeatureHandler
{
// create static factory class that makes an instance
// of this class.
public final static StAXHandlerFactory HSP_HANDLER_FACTORY
=
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new HspHandler(staxenv);
}
};
// local constants
private static final String bitScore = "bitScore";
private static final String score = "score";
private static final String expectValue = "expectValue";
private static final String numberOfIdentities = "numberOfIdentities";
private static final String numberOfPositives = "numberOfPositives";
private static final String alignmentSize = "alignmentSize";
private static final String queryFrame = "queryFrame";
private static final String hitFrame = "hitFrame";
private static final String queryStrand = "queryStrand";
private static final String hitStrand = "hitStrand";
private static final String percentageIdentity = "percentageIdentity";
// class variables
AttributesImpl hspAttrs;
AttributesImpl alignAttrs;
// variables for temp storage
int iNumberOfIdentities = Integer.MIN_VALUE;
int iAlignmentSize = Integer.MIN_VALUE;
String sHsp_qseq = null;
String sHsp_hseq = null;
String sHsp_midline = null;
String sHsp_hit_from = null;
String sHsp_hit_to = null;
String sHsp_query_from = null;
String sHsp_query_to = null;
// constructor
public HspHandler(StAXFeatureHandler staxenv)
{
super(staxenv);
// System.out.println("HspHandler staxenv " + staxenv);
// delegate handling of
// super.addHandler(new ElementRecognizer.ByLocalName("Hsp_num"),
// SubHitPropertyHandler.SUBHIT_PROPERTY_HANDLER_FACTORY);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_bit-score"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
hspAttrs.addAttribute(biojavaUri, bitScore, bitScore, CDATA, s);
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_score"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
hspAttrs.addAttribute(biojavaUri, score, score, CDATA, s);
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_evalue"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
hspAttrs.addAttribute(biojavaUri, expectValue, expectValue, CDATA, s);
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_query-from"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
sHsp_query_from = s.trim();
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_query-to"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
sHsp_query_to = s.trim();
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_hit-from"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
sHsp_hit_from = s.trim();
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_hit-to"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
sHsp_hit_to = s.trim();
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_query-frame"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) throws SAXException {
// save this to compute the percentage identity later.
int frameNo = Integer.parseInt(s.trim());
// convert the frame to the required format and return it
if (hitSequenceType.equals("protein")) {
hspAttrs.addAttribute(biojavaUri, queryFrame, queryFrame, CDATA,
stringifyFrame(frameNo));
}
else if (hitSequenceType.equals("dna")) {
// for some peculiar reason, when Hsp_hit-frame is reversed, it is
// the query frame sequence that is depicted inverted!!
// I assume it works the other way too although that never happens.
hspAttrs.addAttribute(biojavaUri, hitStrand, hitStrand, CDATA,
stringifyStrand(frameNo));
}
else throw new SAXException("illegal sequence type");
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_hit-frame"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) throws SAXException {
// save this to compute the percentage identity later.
int frameNo = Integer.parseInt(s.trim());
// convert the frame to the required format and return it
if (hitSequenceType.equals("protein")) {
hspAttrs.addAttribute(biojavaUri, hitFrame, hitFrame, CDATA,
stringifyFrame(frameNo));
}
else if (hitSequenceType.equals("dna")) {
// for some peculiar reason, when Hsp_hit-frame is reversed, it is
// the query frame sequence that is depicted inverted!!
hspAttrs.addAttribute(biojavaUri, queryStrand, queryStrand, CDATA,
stringifyStrand(frameNo));
}
else throw new SAXException("illegal sequence type");
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_identity"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
iNumberOfIdentities = Integer.parseInt(s.trim());
hspAttrs.addAttribute(biojavaUri, numberOfIdentities, numberOfIdentities, CDATA, s);
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_positive"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
hspAttrs.addAttribute(biojavaUri, numberOfPositives, numberOfPositives, CDATA, s);
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_align-len"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
iAlignmentSize = Integer.parseInt(s.trim());
hspAttrs.addAttribute(biojavaUri, alignmentSize, alignmentSize, CDATA, s);
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_qseq"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
sHsp_qseq = s;
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_hseq"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
sHsp_hseq = s;
}
};
}
}
);
// delegate handling of
super.addHandler(new ElementRecognizer.ByLocalName("Hsp_midline"),
new StAXHandlerFactory() {
public StAXContentHandler getHandler(StAXFeatureHandler staxenv) {
return new StringElementHandlerBase() {
public void setStringValue(String s) {
sHsp_midline = s;
}
};
}
}
);
}
private String stringifyFrame(int frame) throws SAXException {
switch (frame) {
case -3: return "minus3";
case -2: return "minus2";
case -1: return "minus1";
case 1: return "plus1";
case 2: return "plus2";
case 3: return "plus3";
default: throw new SAXException("illegal frame number encountered. ("+frame+")");
}
}
private String stringifyStrand(int strand) throws SAXException {
if (strand > 0) return "plus";
else if (strand < 0) return "minus";
else throw new SAXException("illegal strand number encountered.");
}
public void startElementHandler(
String nsURI,
String localName,
String qName,
Attributes attrs)
throws SAXException
{
// create an AttributesImpl to save the attributes to
hspAttrs = new AttributesImpl();
}
public void endElementHandler(
String nsURI,
String localName,
String qName,
StAXContentHandler handler)
throws SAXException
{
// only generate the element if key parts are present
if ((iNumberOfIdentities == Integer.MIN_VALUE)
|| (iAlignmentSize == Integer.MIN_VALUE)
|| (sHsp_qseq == null)
|| (sHsp_hseq == null)
|| (sHsp_midline == null)
|| (sHsp_hit_from == null)
|| (sHsp_hit_to == null)
|| (sHsp_query_from == null)
|| (sHsp_query_to == null) ) {
throw new SAXException(" is non-compliant.");
}
// compute percentage identity and report it
hspAttrs.addAttribute(biojavaUri,
percentageIdentity,
percentageIdentity,
CDATA,
Float.toString( ((float) (100 * iNumberOfIdentities)) / ((float) iAlignmentSize))
);
// generate start of
staxenv.listener.startElement(biojavaUri, "HSP", biojavaUri + ":HSP", new AttributesImpl());
// generate
staxenv.listener.startElement(biojavaUri, "HSPSummary", biojavaUri + ":" + "HSPSummary", hspAttrs);
staxenv.listener.endElement(biojavaUri, "HSPSummary", biojavaUri + ":" + "HSPSummary");
// generate the
staxenv.listener.startElement(biojavaUri, "BlastLikeAlignment", biojavaUri + ":BlastLikeAlignment", new AttributesImpl());
// generate start of
AttributesImpl queryAttrs = new AttributesImpl();
queryAttrs.addAttribute(biojavaUri, "startPosition", "startPosition", CDATA, sHsp_query_from);
queryAttrs.addAttribute(biojavaUri, "stopPosition", "stopPosition", CDATA, sHsp_query_to);
staxenv.listener.startElement(biojavaUri, "QuerySequence", biojavaUri + ":QuerySequence", queryAttrs);
// pass the sequence symbol tokens over
staxenv.listener.characters(sHsp_qseq.toCharArray(), 0, sHsp_qseq.length());
// generate end of
staxenv.listener.endElement(biojavaUri, "QuerySequence", biojavaUri + ":QuerySequence");
// generate start of
AttributesImpl matchAttrs = new AttributesImpl();
matchAttrs.addAttribute("xml", "space", "xml:space", CDATA, "preserve");
staxenv.listener.startElement(biojavaUri, "MatchConsensus", biojavaUri + ":MatchConsensus", matchAttrs);
// pass the sequence symbol tokens over
staxenv.listener.characters(sHsp_midline.toCharArray(), 0, sHsp_midline.length());
// generate end of
staxenv.listener.endElement(biojavaUri, "MatchConsensus", biojavaUri + ":MatchConsensus");
// generate start of
AttributesImpl hitAttrs = new AttributesImpl();
hitAttrs.addAttribute(biojavaUri, "startPosition", "startPosition", CDATA, sHsp_hit_from);
hitAttrs.addAttribute(biojavaUri, "stopPosition", "stopPosition", CDATA, sHsp_hit_to);
staxenv.listener.startElement(biojavaUri, "HitSequence", "HitSequence", hitAttrs);
// pass the sequence symbol tokens over
staxenv.listener.characters(sHsp_hseq.toCharArray(), 0, sHsp_hseq.length());
// generate end of
staxenv.listener.endElement(biojavaUri, "HitSequence", biojavaUri + ":HitSequence");
// generate end of
staxenv.listener.endElement(biojavaUri, "BlastLikeAlignment", biojavaUri + ":BlastLikeAlignment");
// generate end of
staxenv.listener.endElement(biojavaUri, "HSP", biojavaUri + ":HSP");
}
}
